I guess I would have to get permission from anybody who made changes to lineoperations under the old license.
That is what other projects that have changed licenses did yeah, my glance at git said not many people, and hopefully they will reply yes to a request for permission.
Would changing this license to GPLv3 cause problems in the future?
Doubt it, there is at least one plugin with GPL3 license already (commander) and Geany itself is GPL2+ which is compatible.